Data from: Number of alleles as a predictor of the relative assignment accuracy of STR and SNP baselines for chum salmon

Short tandem repeat (STR) markers, which exhibit many alleles per locus, are commonly used to assign fish to their populations of origin. Single nucleotide polymorphisms (SNPs), which have many technical advantages over STRs, typically exhibit only two alleles per locus. Simulation studies have indicated that number of independent alleles is a good predictor of accuracy of genetic markers for fishery applications. Extant STR baselines for salmon contain hundreds of alleles, and it has been extrapolated that hundreds of SNP markers need to be developed before SNP baselines will compare to these STR baselines. We compared 15 STRs exhibiting 349 independent alleles to 61 SNP assays exhibiting 66 independent alleles for accuracy in assigning to closely related populations of chum salmon. The SNP baseline yielded slightly higher mean accuracies for proportional assignment and comparable accuracies for individual assignment. Overall the SNP baseline performed considerably better, relative to the microsatellite baseline, than predicted based on the number of independent alleles in each baseline. We suggest that this discrepancy is due to the fact that the simulation studies do not capture the impacts of the different strategies commonly employed for discovering and selecting STR and SNP markers.

短串联重复序列（Short tandem repeat, STR）标记在每个位点上携带大量等位基因，是将鱼类个体归至其原产地种群的常用遗传标记。单核苷酸多态性（Single nucleotide polymorphisms, SNPs）相较于STR标记具备诸多技术优势，但通常每个位点仅存在两种等位基因。模拟研究表明，独立等位基因数量可作为渔业应用中遗传标记分型准确性的良好预测指标。现有鲑鱼STR遗传参考基线包含数百个等位基因，据此推断，需开发数百个SNP标记，方能使SNP遗传参考基线的性能比肩上述STR基线。本研究针对狗鲑的近缘种群归群任务，对比了15个总计包含349个独立等位基因的STR标记与61个SNP检测组合（总计包含66个独立等位基因）的分型准确性。结果显示，SNP参考基线在群体比例归群分析中仅展现出略高的平均准确率，而在个体归群分析中则与STR基线准确率相当。总体而言，相较于微卫星参考基线（即STR基线），SNP基线的实际表现远超出基于两者独立等位基因数量的预测结果。我们认为，这一差异的成因在于，现有模拟研究未能涵盖STR与SNP标记在发现及筛选流程中通常采用的不同策略所产生的影响。